Regulation of extreme plasticity in planarian stem cells by mRNA modifications

Project Information

PLANMod

Grant agreement ID: 853640

DOI

10.3030/853640

Project closed

EC signature date 3 October 2019

Start date 1 November 2019

End date 31 October 2025

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 1 487 500,00

EU contribution

€ 1 487 500,00

Coordinated by

TEL AVIV UNIVERSITY
Israel

Periodic Reporting for period 4 - PLANMod (Regulation of extreme plasticity in planarian stem cells by mRNA modifications)

Reporting period: 2024-05-01 to 2025-10-31

Summary of the context and overall objectives of the project

Regeneration, the growth of new tissues following injuries, is widespread in the animal kingdom, yet most mammals have a very limited ability to regenerate organs. Planarians, freshwater flatworms, can regrow any missing body part, including an entire brain, using a large population of pluripotent stem cells. The PLANMod project investigated the mechanisms that regulate these stem cells to facilitate tissue production on demand. Our research focused on N6-methyladenosine (m6A), a biochemical modification to RNA that is abundant across all life forms.

We discovered that this modification acts as a critical "checkpoint" for stem cells. While m6A is not required for stem cells to survive, it is essential for them to differentiate, the process of becoming specialized tissue cells. Unexpectedly, we found that this RNA pathway communicates with the machinery that remodels the DNA packaging (chromatin), ensuring the nucleus is organized, which is essential for supporting cell fate changes.

Furthermore, we proposed a new model for the evolution of this modification. By mapping m6A at high resolution, we found that the "rules" for placing these marks on RNA are based on simple sequence patterns. This simplicity makes the system highly flexible, allowing different species to rapidly evolve unique ways to regulate their genes using the same basic machinery. Overall, PLANMod revealed fundamental principles of how RNA biochemistry contributes to animal regeneration.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

We systematically analyzed the function of every known gene involved in the m6A pathway and examined its roles in the maintenance of tissues, regeneration, and stem cell regulation. To achieve this, we established new experimental and computational methodologies, including PlanaTools and high-resolution mapping techniques. The work resulted in the first single-nucleotide resolution maps of m6A in planarians and a comprehensive analysis of how inhibiting the pathway affects these sites.

Our analysis demonstrated that m6A is essential for the production of certain tissues by stem cells (differentiation), but not for stem cell viability. Therefore, the most dramatic outcome of inhibiting the m6A pathway, death, is a consequence of defects in tissue production rather than a lack of stem cells. This highlights similarities between early mammalian development and the regulation of adult stem cells in planarians.

We further discovered that defects in tissue production lead to the emergence of abnormal cells that molecularly resemble neuronal progenitors. Systematic computational efforts unraveled that similar cells appear following the inactivation of the NuRD complex, a cellular machine crucial for packaging DNA. We confirmed that the m6A pathway and NuRD function together to physically condense DNA, protecting the genome during the stress of regeneration.

Finally, our precise mapping led to a new model for the evolution of this modification. We found that the instructions for placing m6A are based on simple sequence rules. This simplicity allows the "epitranscriptomic code" to be highly flexible, enabling organisms to easily acquire or lose regulatory sites during evolution to adapt their gene regulation strategies.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

Our results have defined the m6A modification as a critical checkpoint for stem cell differentiation. We demonstrated that a small biochemical change to RNA molecules is required for the "decision" of a stem cell to transform into a specialized tissue cell. We advanced significantly beyond the state of the art by demonstrating the association between RNA and DNA packaging. We identified that the m6A pathway regulates the NuRD chromatin remodeling complex. We discovered that this interaction impacts the nuclear organization: these pathways output is associated with the condensation of DNA, impacting critical processes like cell division.

Furthermore, we established a new evolutionary model for this pathway. We found that the "rules" for placing m6A marks are simple and flexible, allowing different species to easily adapt their genetic regulation during evolution. Finally, we pushed the technological boundaries of the field by developing a browser-based engine that allows the analysis of complex genomic data without the need for advanced coding skills, thereby democratizing access to biological research.

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